Comments (12)
I can see the tomo programs are located - in a relion/src/tomography_python_programs - ie there an environment variable to point to this? Currently it is looking at the conda environment to locate the programs.
nora
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I'm having the same problem, did you figure out how to fix it?
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The files are successfully made in the bin directory, but we still get the python error.
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Hi @nbcronin, No, dynamight is functional, but the other tomo python programs do not. The conda paths are fine, Relion is able to find the correct python path during compilation and any other tools except for the tomo tools.
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@biochem-fan Any ideas?
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hello,
had the same problem with relion-5.0 and found that among this python module some other are missing,
I fixed it by.
# used by relion_python_tomo_align_tilt_series
cd $(SOFT)/src && cp -r tomography_python_programs $(PYLIB)
$(PIP) install makefun yet_another_imod_wrapper lil_aretomo
# used by relion_python_tomo_get_particle_poses
$(PIP) install morphosamplers
# used by relion_python_tomo_pick
$(PIP) install napari_threedee
# used by relion_python_tomo_pick relion_python_tomo_view relion_python_tomo_exclude_tilt_images
$(PIP) install lru-dict
NB installation performed out of conda.
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Hi @nbcronin
Unfortunately, it still doesn't work.
---------------------------------- PYTHON ERROR ---------------------------------
Has RELION been provided a Python interpreter with the correct environment?
The interpreter can be passed to RELION either during Cmake configuration by
using the Cmake flag -DPYTHON_EXE_PATH=<path/to/python/interpreter>.
---------------------------------------------------------------------------------
The above error appears specifically on relion_python_tomo_import
, relion_python_tomo_denoise
, relion_python_tomo_exclude_tilt_images
, relion_python_modelangelo
, relion_python_topaz
, and relion_python_tomo_align_tilt_series
. The other python tools are fine.
@biochem-fan Can you please provide an update on this?
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@Qiangong2 I am not involved in the tomography aspect of RELION, so I cannot help.
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@Qiangong2 I am not involved in the tomography aspect of RELION, so I cannot help.
@biochem-fan Who is then?
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Related Issues (20)
- relion5 centered coordinate definition HOT 2
- Possible fix for Qt error when opening napari from RELION
- Refine3D fails to setup MPI correctly HOT 9
- Typo in tomograms.star in Relion 5 tomo tutorial?
- Tilt angle offset being undone when aligning TS with IMOD
- Use of Relion Logo in supplemental figure in scientific paper
- Bad Extracted Particles with Edge and Fringe Artefacts HOT 1
- Does RELION 5.0 support the GCTF library? HOT 1
- Relion 5.0 Aretomo not working HOT 2
- DynaMight optimize deformations - training exceeds specified number of epochs
- Error with relion5 using 2D classification on aws g6 instances HOT 1
- Relion/5.0 tomgoraphy Reconstruction modality runs in an endless loop HOT 2
- AreTomo executable was not found HOT 3
- relion_tomo_reconstruct_tomogram_mpi requiring more memory than before and then crashing HOT 2
- Proxy error during build HOT 1
- Refine auto 3D error: Helical reconstruction HOT 1
- Segmentation Fault relion_refine_mpi HOT 5
- Denoise Tomograms with continue Flag HOT 1
- Align tilt-series additional arguments HOT 4
- Import Problem: no such option: -optics-group-name
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